BioSQL.Loader.DatabaseLoader

Package BioSQL :: Module Loader :: Class DatabaseLoader

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Class DatabaseLoader

Load a database with biopython objects.

Method Summary
	`__init__(self, adaptor, dbid)` Initialize with connection information for the database.
	`load_seqrecord(self, record)` Load a Biopython SeqRecord into the database.
	`_add_dbxref(self, dbname, accession, version)` Insert a dbxref and return its id
	`_get_ontology_id(self, name, definition)`
	`_get_taxon_id(self, record)` Get the id corresponding to a taxon.
	`_get_term_id(self, name, ontology_id, definition, identifier)` Get the id that corresponds to a term.
	`_insert_seqfeature_location(self, feature, rank, seqfeature_id)` Add a location of a SeqFeature to the seqfeature_location table.
	`_load_bioentry_date(self, record, bioentry_id)` Add the effective date of the entry into the database.
	`_load_bioentry_table(self, record)` Fill the bioentry table with sequence information.
	`_load_biosequence(self, record, bioentry_id)` Load the biosequence table in the database.
	`_load_comment(self, record, bioentry_id)`
	`_load_reference(self, reference, rank, bioentry_id)`
	`_load_seqfeature(self, feature, feature_rank, bioentry_id)` Load a biopython SeqFeature into the database.
	`_load_seqfeature_basic(self, feature_type, feature_rank, bioentry_id)` Load the first tables of a seqfeature and returns the id.
	`_load_seqfeature_locations(self, feature, seqfeature_id)` Load all of the locations for a SeqFeature into tables.
	`_load_seqfeature_qualifiers(self, qualifiers, seqfeature_id)` Insert the (key, value) pair qualifiers relating to a feature.

Method Details

init(self, adaptor, dbid)
(Constructor)

Initialize with connection information for the database.

XXX Figure out what I need to load a database and document it.

load_seqrecord(self, record)

Load a Biopython SeqRecord into the database.

_add_dbxref(self, dbname, accession, version)

Insert a dbxref and return its id

_get_taxon_id(self, record)

Get the id corresponding to a taxon.

If the species isn't in the taxon table, it is created.

_get_term_id(self, name, ontology_id=None, definition=None, identifier=None)

Get the id that corresponds to a term.

This looks through the term table for a the given term. If it is not found, a new id corresponding to this term is created. In either case, the id corresponding to that term is returned, so that you can reference it in another table.

The ontology_id should be used to disambiguate the term.

_insert_seqfeature_location(self, feature, rank, seqfeature_id)

Add a location of a SeqFeature to the seqfeature_location table.

_load_bioentry_date(self, record, bioentry_id)

Add the effective date of the entry into the database.

_load_bioentry_table(self, record)

Fill the bioentry table with sequence information.

_load_biosequence(self, record, bioentry_id)

Load the biosequence table in the database.

_load_seqfeature(self, feature, feature_rank, bioentry_id)

Load a biopython SeqFeature into the database.

_load_seqfeature_basic(self, feature_type, feature_rank, bioentry_id)

Load the first tables of a seqfeature and returns the id.

This loads the "key" of the seqfeature (ie. CDS, gene) and the basic seqfeature table itself.

_load_seqfeature_locations(self, feature, seqfeature_id)

Load all of the locations for a SeqFeature into tables.

This adds the locations related to the SeqFeature into the
seqfeature_location table. Fuzzies are not handled right now.
For a simple location, ie (1..2), we have a single table row
with seq_start = 1, seq_end = 2, location_rank = 1.

For split locations, ie (1..2, 3..4, 5..6) we would have three
row tables with:
    start = 1, end = 2, rank = 1
    start = 3, end = 4, rank = 2
    start = 5, end = 6, rank = 3

_load_seqfeature_qualifiers(self, qualifiers, seqfeature_id)

Insert the (key, value) pair qualifiers relating to a feature.

Qualifiers should be a dictionary of the form:
    {key : [value1, value2]}

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